Current Design
Currently, the way of controlling the system role permissions for Custom Hierarchies is different than the other system role permissions.
Go to Administration > Other Setup > Custom Hierarchies and you need to toggle off the main toggle to set up the role level privileges.,

After toggling off the main "Custom Hierarchies" toggle now you can go to Manage and from there, you can select whether people can view the custom rooms and which levels OR if they can create and edit the rooms (adding additional values for a level, etc)

If the main toggle is ON in the system role, the user can manage and delete entire Custom Hierarchies.

Enhancement Request
Improve the current role permission setup of the Custom Hierarchies and/or change it to how other role permission toggles work. In the current design, if the main toggle is ON, all users can access the Admin menu and delete the Custom Hierarchies. 

Also, please add granular membership permissions for Custom Hierarchies like the other system role permission toggles. It would also be helpful if the permission were per the portfolio as well.

Regards